Premankar,
Since you cannot increase the X2 capacitor, can you try increasing the DC bus capacitor and see what changes it provides.
Also, could you increase C16 and C17. Recommended value is 4.7uF each (this may affect the PF, but the PF may not be an issue, as the power is very small). If this still does not resolve the CE issues add differential inductors in between as shown below.
Please let us know the results of these changes.
Thank You,
Ramon